Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_012385734.1 BIND_RS14190 ornithine--oxo-acid transaminase
Query= curated2:P59318 (401 letters) >NCBI__GCF_000019845.1:WP_012385734.1 Length = 412 Score = 282 bits (722), Expect = 1e-80 Identities = 159/384 (41%), Positives = 219/384 (57%), Gaps = 10/384 (2%) Query: 23 VQKAKRHLLQNYKQPPFVLARGQGARVWDMDGREYLDLIGGIATCALGHCHPEVVAAAKA 82 + + +R NY P VL+ GQGA ++D DGR YLD++ + + GH HP +V A K Sbjct: 6 IDQEERFGAHNYAPLPVVLSHGQGAFLFDCDGRRYLDMMSAYSAASFGHLHPRLVGALKR 65 Query: 83 QLDSLWHVSNVFYSQPQIDLAAQLTEWSGLSRAFFCNSGAEANEALLKLTRKVMKDR-GT 141 QL+ L VS +++ L +GL N+GAEA E +K R+ DR Sbjct: 66 QLERLDLVSRAYHTDTLGPFCEDLARLTGLDACLPMNTGAEAVETAIKAARRYGYDRLSI 125 Query: 142 PE-RFEVISFDSSFHGRTLATVTATGQAKYQKGFEPLPAGFTHVPYGDLEAVRKAVGPAT 200 PE + E+I +FHGRT + + A ++GF P GF VP+GD A+ AVGP T Sbjct: 126 PEDQAEIIVAAGNFHGRTTTIIGFSSDAATRRGFGPFAPGFVLVPFGDAGALEAAVGPRT 185 Query: 201 AAILVEPIQGEGGVRMAPLGFLVGLRALCDEHGLLLLVDEVQTGMGRTGKPFGFMHEGIV 260 AA+L+EPIQGE G+ + P G+L LR LCD HG+LL+ DEVQ+G GRTG+ F F HEG Sbjct: 186 AAVLIEPIQGEAGIILPPPGYLAALRRLCDRHGILLIFDEVQSGFGRTGRTFAFEHEGAK 245 Query: 261 PDGISVAKALGNG-LPIGAMLCKEELGASLTPGTHGSTFGGNPVAAAAANAVVRILRRPG 319 PDG+ + KALG G LP+ A K L PG+HGSTFGGNP+A A A + +L+ Sbjct: 246 PDGLILGKALGGGLLPVSAFAAKRSLMDVFDPGSHGSTFGGNPLAMAVAREAMHVLQEEH 305 Query: 320 FLDEVQEKGAYLLARARELQGRLPAGRIQAVRGQGLLVGVQLDHKVA---PVIAQVHEEG 376 ++ ++ G LL R + PA + AVRG+GL GV LD +A V ++ E G Sbjct: 306 LVERSEKLGGVLLDALRAIDH--PA--VLAVRGKGLWAGVDLDPALADAKKVCLKMMERG 361 Query: 377 LLVNPAGDRTMLFAPPFIVTVREL 400 +L T+ FAPP ++T +L Sbjct: 362 VLTKETHATTIRFAPPLVITEADL 385 Lambda K H 0.319 0.136 0.404 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 486 Number of extensions: 24 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 401 Length of database: 412 Length adjustment: 31 Effective length of query: 370 Effective length of database: 381 Effective search space: 140970 Effective search space used: 140970 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory